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Joseph F. Rudzinski
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Coarse-graining entropy, forces, and structures
JF Rudzinski, WG Noid
The Journal of chemical physics 135 (21), 214101, 2011
1692011
Influence of Target Concentration and Background Binding on In Vitro Selection of Affinity Reagents
J Wang, JF Rudzinski, Q Gong, HT Soh, PJ Atzberger
Public Library of Science 7 (8), e43940, 2012
902012
Investigation of Coarse-Grained Mappings via an Iterative Generalized Yvon–Born–Green Method
JF Rudzinski, WG Noid
The Journal of Physical Chemistry B 118 (28), 8295-8312, 2014
722014
Bottom-up coarse-graining of peptide ensembles and helix–coil transitions
JF Rudzinski, WG Noid
Journal of chemical theory and computation 11 (3), 1278-1291, 2015
672015
Recent progress towards chemically-specific coarse-grained simulation models with consistent dynamical properties
JF Rudzinski
Computation 7 (3), 42, 2019
562019
The role of many-body correlations in determining potentials for coarse-grained models of equilibrium structure
JF Rudzinski, WG Noid
The Journal of Physical Chemistry B 116 (29), 8621-8635, 2012
552012
BOCS: Bottom-Up Open-Source Coarse-Graining Software
NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid
The Journal of Physical Chemistry B, 2017
522017
Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders
YB Varolgüneş, T Bereau, JF Rudzinski
Machine Learning: Science and Technology 1 (1), 015012, 2020
482020
A generalized-Yvon-Born-Green method for coarse-grained modeling
JF Rudzinski, WG Noid
The European Physical Journal Special Topics 224 (12), 2193-2216, 2015
472015
Scaling behavior and local structure of ion aggregates in single-ion conductors
K Lu, JF Rudzinski, WG Noid, ST Milner, JK Maranas
Soft Matter 10 (7), 978-989, 2014
402014
Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information
JF Rudzinski, K Kremer, T Bereau
The Journal of chemical physics 144 (5), 051102, 2016
362016
Generalized‐Yvon–Born–Green Model of Toluene
CR Ellis, JF Rudzinski, WG Noid
Macromolecular Theory and Simulations 20 (7), 478-495, 2011
292011
Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics
T Bereau, JF Rudzinski
Physical Review Letters 121 (25), 256002, 2018
282018
Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields
JF Rudzinski, T Bereau
The European Physical Journal Special Topics 225 (8-9), 1373-1389, 2016
212016
Extended Ensemble Approach to Transferable Potentials for Low-Resolution Coarse-Grained Models of Ionomers
JF Rudzinski, K Lu, ST Milner, JK Maranas, WG Noid
Journal of Chemical Theory and Computation 13 (5), 2185-2201, 2017
202017
Coarse-grained conformational surface hopping: Methodology and transferability
JF Rudzinski, T Bereau
The Journal of Chemical Physics 153 (21), 214110, 2020
152020
Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model
Y Zhao, R Cortes-Huerto, K Kremer, JF Rudzinski
The Journal of Physical Chemistry B 124 (20), 4097-4113, 2020
112020
NOMAD: A distributed web-based platform for managing materials science research data
M Scheidgen, L Himanen, AN Ladines, D Sikter, M Nakhaee, Á Fekete, ...
Journal of Open Source Software 8 (90), 5388, 2023
102023
Dynamical properties across different coarse-grained models for ionic liquids
JF Rudzinski, S Kloth, S Wörner, T Pal, K Kremer, T Bereau, M Vogel
Journal of Physics: Condensed Matter 33 (22), 224001, 2021
92021
Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations
SJ Wörner, T Bereau, K Kremer, JF Rudzinski
The Journal of Chemical Physics 151 (24), 244110, 2019
92019
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Articles 1–20